Starting phenix.real_space_refine on Wed Feb 12 04:50:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6h_37323/02_2025/8w6h_37323.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6h_37323/02_2025/8w6h_37323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w6h_37323/02_2025/8w6h_37323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6h_37323/02_2025/8w6h_37323.map" model { file = "/net/cci-nas-00/data/ceres_data/8w6h_37323/02_2025/8w6h_37323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6h_37323/02_2025/8w6h_37323.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.119 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 Na 2 4.78 5 C 4897 2.51 5 N 1098 2.21 5 O 1219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7268 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3601 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 28, 'TRANS': 433} Chain breaks: 4 Chain: "B" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3599 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 27, 'TRANS': 433} Chain breaks: 4 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' NA': 1, 'CLR': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' NA': 1, 'CLR': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.57, per 1000 atoms: 0.63 Number of scatterers: 7268 At special positions: 0 Unit cell: (96.743, 84.786, 79.351, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 Na 2 11.00 O 1219 8.00 N 1098 7.00 C 4897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 73.1% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 15 through 23 removed outlier: 3.979A pdb=" N LEU A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 removed outlier: 3.519A pdb=" N CYS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 60 Processing helix chain 'A' and resid 61 through 70 Proline residue: A 67 - end of helix Processing helix chain 'A' and resid 83 through 102 removed outlier: 3.555A pdb=" N GLY A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 98 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 116 removed outlier: 3.785A pdb=" N VAL A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 removed outlier: 3.817A pdb=" N LEU A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 160 removed outlier: 4.042A pdb=" N MET A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 236 through 251 removed outlier: 3.734A pdb=" N THR A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.593A pdb=" N PHE A 265 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 266 " --> pdb=" O ASN A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 308 removed outlier: 3.517A pdb=" N PHE A 285 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.890A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.649A pdb=" N LYS A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 364 removed outlier: 3.989A pdb=" N ILE A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.869A pdb=" N VAL A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 431 removed outlier: 3.503A pdb=" N SER A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.863A pdb=" N ILE A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 461 removed outlier: 3.746A pdb=" N LYS A 461 " --> pdb=" O TRP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.548A pdb=" N GLY A 466 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 467 " --> pdb=" O PRO A 464 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 468 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 removed outlier: 3.542A pdb=" N ILE A 473 " --> pdb=" O PRO A 469 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET A 480 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 508 removed outlier: 3.664A pdb=" N PHE A 497 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 498 " --> pdb=" O ILE A 494 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 3.524A pdb=" N SER A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Proline residue: A 503 - end of helix removed outlier: 3.600A pdb=" N GLU A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 521 Proline residue: A 518 - end of helix Processing helix chain 'A' and resid 534 through 539 removed outlier: 3.554A pdb=" N ILE A 538 " --> pdb=" O PRO A 534 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 534 through 539' Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 547 through 572 removed outlier: 3.539A pdb=" N VAL A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'B' and resid 15 through 23 removed outlier: 3.979A pdb=" N LEU B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 50 removed outlier: 3.518A pdb=" N CYS B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 46 " --> pdb=" O PHE B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 60 Processing helix chain 'B' and resid 61 through 70 Proline residue: B 67 - end of helix Processing helix chain 'B' and resid 83 through 102 removed outlier: 3.554A pdb=" N GLY B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER B 98 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.785A pdb=" N VAL B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 removed outlier: 3.816A pdb=" N LEU B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 160 removed outlier: 4.042A pdb=" N MET B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 236 through 251 removed outlier: 3.733A pdb=" N THR B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 removed outlier: 3.593A pdb=" N PHE B 265 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 266 " --> pdb=" O ASN B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 308 removed outlier: 3.518A pdb=" N PHE B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Proline residue: B 290 - end of helix removed outlier: 3.890A pdb=" N ILE B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.650A pdb=" N LYS B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 364 removed outlier: 3.988A pdb=" N ILE B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.869A pdb=" N VAL B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 431 removed outlier: 3.502A pdb=" N SER B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 452 removed outlier: 3.862A pdb=" N ILE B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 452 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 461 removed outlier: 3.746A pdb=" N LYS B 461 " --> pdb=" O TRP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.549A pdb=" N GLY B 466 " --> pdb=" O SER B 463 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 467 " --> pdb=" O PRO B 464 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 468 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 485 removed outlier: 3.542A pdb=" N ILE B 473 " --> pdb=" O PRO B 469 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET B 480 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 508 removed outlier: 3.665A pdb=" N PHE B 497 " --> pdb=" O THR B 493 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 498 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Proline residue: B 499 - end of helix removed outlier: 3.524A pdb=" N SER B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Proline residue: B 503 - end of helix removed outlier: 3.601A pdb=" N GLU B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 521 Proline residue: B 518 - end of helix Processing helix chain 'B' and resid 534 through 539 removed outlier: 3.554A pdb=" N ILE B 538 " --> pdb=" O PRO B 534 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 534 through 539' Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 546 through 572 removed outlier: 3.921A pdb=" N MET B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS B 570 " --> pdb=" O MET B 566 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.792A pdb=" N SER A 419 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 400 through 402 removed outlier: 6.793A pdb=" N SER B 419 " --> pdb=" O ALA B 401 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1049 1.29 - 1.42: 1957 1.42 - 1.55: 4385 1.55 - 1.68: 2 1.68 - 1.81: 82 Bond restraints: 7475 Sorted by residual: bond pdb=" C16 CLR B 603 " pdb=" C17 CLR B 603 " ideal model delta sigma weight residual 1.554 1.442 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C16 CLR A 603 " pdb=" C17 CLR A 603 " ideal model delta sigma weight residual 1.554 1.442 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C13 CLR B 603 " pdb=" C14 CLR B 603 " ideal model delta sigma weight residual 1.537 1.426 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C13 CLR A 603 " pdb=" C14 CLR A 603 " ideal model delta sigma weight residual 1.537 1.427 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C THR B 259 " pdb=" O THR B 259 " ideal model delta sigma weight residual 1.233 1.162 0.071 1.30e-02 5.92e+03 2.95e+01 ... (remaining 7470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 9822 2.61 - 5.21: 310 5.21 - 7.82: 72 7.82 - 10.43: 21 10.43 - 13.04: 10 Bond angle restraints: 10235 Sorted by residual: angle pdb=" C THR A 259 " pdb=" CA THR A 259 " pdb=" CB THR A 259 " ideal model delta sigma weight residual 110.45 118.40 -7.95 1.73e+00 3.34e-01 2.11e+01 angle pdb=" C THR B 259 " pdb=" CA THR B 259 " pdb=" CB THR B 259 " ideal model delta sigma weight residual 110.45 118.08 -7.63 1.73e+00 3.34e-01 1.95e+01 angle pdb=" C16 CLR B 603 " pdb=" C17 CLR B 603 " pdb=" C20 CLR B 603 " ideal model delta sigma weight residual 112.02 98.98 13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" C16 CLR A 603 " pdb=" C17 CLR A 603 " pdb=" C20 CLR A 603 " ideal model delta sigma weight residual 112.02 99.01 13.01 3.00e+00 1.11e-01 1.88e+01 angle pdb=" N ASN B 119 " pdb=" CA ASN B 119 " pdb=" C ASN B 119 " ideal model delta sigma weight residual 111.53 120.92 -9.39 2.18e+00 2.10e-01 1.86e+01 ... (remaining 10230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 3874 15.99 - 31.99: 454 31.99 - 47.98: 82 47.98 - 63.97: 2 63.97 - 79.96: 10 Dihedral angle restraints: 4422 sinusoidal: 1735 harmonic: 2687 Sorted by residual: dihedral pdb=" CA ASN A 119 " pdb=" C ASN A 119 " pdb=" N PRO A 120 " pdb=" CA PRO A 120 " ideal model delta harmonic sigma weight residual 180.00 139.58 40.42 0 5.00e+00 4.00e-02 6.53e+01 dihedral pdb=" CA ASN B 119 " pdb=" C ASN B 119 " pdb=" N PRO B 120 " pdb=" CA PRO B 120 " ideal model delta harmonic sigma weight residual 180.00 139.58 40.42 0 5.00e+00 4.00e-02 6.53e+01 dihedral pdb=" CA PRO B 27 " pdb=" C PRO B 27 " pdb=" N ILE B 28 " pdb=" CA ILE B 28 " ideal model delta harmonic sigma weight residual 180.00 149.61 30.39 0 5.00e+00 4.00e-02 3.69e+01 ... (remaining 4419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1109 0.094 - 0.189: 125 0.189 - 0.283: 8 0.283 - 0.377: 6 0.377 - 0.471: 4 Chirality restraints: 1252 Sorted by residual: chirality pdb=" C10 CLR A 603 " pdb=" C1 CLR A 603 " pdb=" C5 CLR A 603 " pdb=" C9 CLR A 603 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" C10 CLR B 603 " pdb=" C1 CLR B 603 " pdb=" C5 CLR B 603 " pdb=" C9 CLR B 603 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 1249 not shown) Planarity restraints: 1195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 534 " 0.074 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO B 535 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO B 535 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 535 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 534 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO A 535 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " -0.050 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A 27 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " -0.044 5.00e-02 4.00e+02 ... (remaining 1192 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1122 2.74 - 3.28: 6646 3.28 - 3.82: 11202 3.82 - 4.36: 14235 4.36 - 4.90: 24319 Nonbonded interactions: 57524 Sorted by model distance: nonbonded pdb=" O CYS A 243 " pdb=" OG SER A 247 " model vdw 2.205 3.040 nonbonded pdb=" O CYS B 243 " pdb=" OG SER B 247 " model vdw 2.205 3.040 nonbonded pdb=" O TRP A 284 " pdb=" OG SER A 288 " model vdw 2.228 3.040 nonbonded pdb=" O TRP B 284 " pdb=" OG SER B 288 " model vdw 2.228 3.040 nonbonded pdb=" O PHE B 42 " pdb=" OG1 THR B 46 " model vdw 2.274 3.040 ... (remaining 57519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 308 or resid 333 through 364 or resid 381 throug \ h 588 or resid 601 through 603)) selection = (chain 'B' and (resid 9 through 161 or resid 233 through 588 or resid 601 throug \ h 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.830 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.112 7475 Z= 0.689 Angle : 1.230 13.037 10235 Z= 0.617 Chirality : 0.070 0.471 1252 Planarity : 0.011 0.110 1195 Dihedral : 13.789 79.965 2674 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.52 % Favored : 90.25 % Rotamer: Outliers : 0.76 % Allowed : 9.19 % Favored : 90.05 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.00 (0.15), residues: 903 helix: -4.58 (0.08), residues: 668 sheet: None (None), residues: 0 loop : -3.89 (0.32), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 572 HIS 0.011 0.003 HIS B 105 PHE 0.028 0.002 PHE A 354 TYR 0.011 0.002 TYR A 81 ARG 0.003 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.891 Fit side-chains REVERT: A 65 MET cc_start: 0.8834 (mtp) cc_final: 0.8578 (mtp) REVERT: A 344 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7576 (mtp85) REVERT: B 65 MET cc_start: 0.8735 (mtp) cc_final: 0.8460 (mtp) REVERT: B 68 MET cc_start: 0.7694 (mtm) cc_final: 0.7453 (mtm) REVERT: B 344 ARG cc_start: 0.7816 (mtp180) cc_final: 0.7570 (mtp85) outliers start: 6 outliers final: 0 residues processed: 139 average time/residue: 0.1996 time to fit residues: 37.2558 Evaluate side-chains 111 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 304 GLN B 160 ASN B 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.127798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.104313 restraints weight = 9189.230| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.56 r_work: 0.2993 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7475 Z= 0.219 Angle : 0.753 11.458 10235 Z= 0.378 Chirality : 0.045 0.241 1252 Planarity : 0.008 0.085 1195 Dihedral : 6.859 57.713 1085 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.39 % Allowed : 11.08 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.24), residues: 903 helix: -2.22 (0.17), residues: 625 sheet: None (None), residues: 0 loop : -2.57 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 572 HIS 0.007 0.001 HIS B 105 PHE 0.013 0.001 PHE A 287 TYR 0.012 0.002 TYR A 81 ARG 0.007 0.001 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.843 Fit side-chains REVERT: A 157 GLN cc_start: 0.8286 (mt0) cc_final: 0.7897 (mt0) REVERT: B 65 MET cc_start: 0.9236 (mtp) cc_final: 0.8974 (mtp) outliers start: 19 outliers final: 12 residues processed: 131 average time/residue: 0.1696 time to fit residues: 31.1700 Evaluate side-chains 125 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103720 restraints weight = 9421.107| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.59 r_work: 0.2990 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7475 Z= 0.217 Angle : 0.674 10.051 10235 Z= 0.335 Chirality : 0.044 0.235 1252 Planarity : 0.006 0.076 1195 Dihedral : 6.039 55.012 1085 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.77 % Allowed : 13.22 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.28), residues: 903 helix: -1.01 (0.21), residues: 647 sheet: None (None), residues: 0 loop : -2.40 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 572 HIS 0.009 0.001 HIS A 105 PHE 0.015 0.001 PHE A 287 TYR 0.023 0.002 TYR A 514 ARG 0.006 0.001 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.838 Fit side-chains REVERT: A 71 ILE cc_start: 0.8512 (mm) cc_final: 0.8271 (mt) REVERT: A 157 GLN cc_start: 0.8427 (mt0) cc_final: 0.8099 (mt0) REVERT: B 34 GLU cc_start: 0.7529 (pm20) cc_final: 0.7096 (mp0) REVERT: B 267 GLU cc_start: 0.8710 (tp30) cc_final: 0.8472 (mm-30) outliers start: 22 outliers final: 10 residues processed: 134 average time/residue: 0.1557 time to fit residues: 29.9902 Evaluate side-chains 123 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 384 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 49 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.105969 restraints weight = 9361.922| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.58 r_work: 0.3014 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7475 Z= 0.192 Angle : 0.638 8.978 10235 Z= 0.316 Chirality : 0.042 0.233 1252 Planarity : 0.005 0.070 1195 Dihedral : 5.522 44.375 1085 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.77 % Allowed : 15.74 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.29), residues: 903 helix: -0.39 (0.22), residues: 647 sheet: None (None), residues: 0 loop : -2.25 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 572 HIS 0.007 0.001 HIS A 105 PHE 0.013 0.001 PHE B 287 TYR 0.023 0.001 TYR B 514 ARG 0.006 0.001 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.861 Fit side-chains REVERT: A 34 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: A 294 ILE cc_start: 0.9036 (mt) cc_final: 0.8780 (mt) REVERT: B 34 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: B 267 GLU cc_start: 0.8649 (tp30) cc_final: 0.8432 (mm-30) REVERT: B 294 ILE cc_start: 0.9063 (mt) cc_final: 0.8825 (mt) outliers start: 22 outliers final: 17 residues processed: 127 average time/residue: 0.1564 time to fit residues: 28.4277 Evaluate side-chains 131 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 58 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.104515 restraints weight = 9248.666| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.57 r_work: 0.2995 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7475 Z= 0.223 Angle : 0.645 8.941 10235 Z= 0.318 Chirality : 0.044 0.230 1252 Planarity : 0.005 0.068 1195 Dihedral : 5.291 35.964 1085 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.53 % Allowed : 15.87 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.30), residues: 903 helix: -0.13 (0.22), residues: 653 sheet: None (None), residues: 0 loop : -2.06 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.009 0.001 HIS B 105 PHE 0.015 0.001 PHE B 287 TYR 0.026 0.002 TYR A 514 ARG 0.002 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.783 Fit side-chains REVERT: A 34 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: A 267 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7760 (tm-30) REVERT: A 294 ILE cc_start: 0.9052 (mt) cc_final: 0.8797 (mt) REVERT: A 484 LEU cc_start: 0.9055 (tp) cc_final: 0.8689 (tt) REVERT: B 34 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: B 267 GLU cc_start: 0.8627 (tp30) cc_final: 0.8406 (mm-30) REVERT: B 294 ILE cc_start: 0.9062 (mt) cc_final: 0.8824 (mt) REVERT: B 484 LEU cc_start: 0.9034 (tp) cc_final: 0.8680 (tt) outliers start: 28 outliers final: 21 residues processed: 129 average time/residue: 0.1586 time to fit residues: 29.1751 Evaluate side-chains 133 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 59 optimal weight: 0.0270 chunk 77 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.0010 chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 overall best weight: 0.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.108754 restraints weight = 9064.461| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.57 r_work: 0.3028 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7475 Z= 0.184 Angle : 0.644 14.337 10235 Z= 0.310 Chirality : 0.043 0.229 1252 Planarity : 0.005 0.065 1195 Dihedral : 5.072 31.587 1085 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.65 % Allowed : 15.74 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.30), residues: 903 helix: 0.13 (0.22), residues: 651 sheet: None (None), residues: 0 loop : -2.05 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 572 HIS 0.007 0.001 HIS B 105 PHE 0.012 0.001 PHE B 287 TYR 0.025 0.001 TYR B 514 ARG 0.002 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.774 Fit side-chains REVERT: A 34 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: A 243 CYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8295 (p) REVERT: A 267 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7742 (tm-30) REVERT: A 294 ILE cc_start: 0.9047 (mt) cc_final: 0.8799 (mt) REVERT: A 484 LEU cc_start: 0.9035 (tp) cc_final: 0.8652 (tt) REVERT: B 11 ARG cc_start: 0.7424 (mmp80) cc_final: 0.7186 (mmp80) REVERT: B 34 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: B 267 GLU cc_start: 0.8546 (tp30) cc_final: 0.8311 (mm-30) REVERT: B 294 ILE cc_start: 0.9057 (mt) cc_final: 0.8831 (mt) REVERT: B 484 LEU cc_start: 0.9019 (tp) cc_final: 0.8655 (tt) outliers start: 29 outliers final: 21 residues processed: 135 average time/residue: 0.1554 time to fit residues: 30.0268 Evaluate side-chains 144 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN B 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.131721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.107975 restraints weight = 9084.857| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.53 r_work: 0.3028 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7475 Z= 0.200 Angle : 0.643 12.553 10235 Z= 0.310 Chirality : 0.043 0.224 1252 Planarity : 0.005 0.065 1195 Dihedral : 5.000 30.886 1085 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.27 % Allowed : 15.99 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.30), residues: 903 helix: 0.20 (0.22), residues: 661 sheet: None (None), residues: 0 loop : -1.99 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.007 0.001 HIS B 105 PHE 0.013 0.001 PHE A 287 TYR 0.025 0.002 TYR B 514 ARG 0.001 0.000 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.878 Fit side-chains REVERT: A 34 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: A 243 CYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8402 (p) REVERT: A 294 ILE cc_start: 0.9060 (mt) cc_final: 0.8828 (mt) REVERT: A 484 LEU cc_start: 0.9043 (tp) cc_final: 0.8670 (tt) REVERT: B 11 ARG cc_start: 0.7444 (mmp80) cc_final: 0.7174 (mmp80) REVERT: B 34 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: B 65 MET cc_start: 0.9266 (mtp) cc_final: 0.8997 (mtp) REVERT: B 294 ILE cc_start: 0.9062 (mt) cc_final: 0.8849 (mt) REVERT: B 484 LEU cc_start: 0.9063 (tp) cc_final: 0.8679 (tt) outliers start: 26 outliers final: 22 residues processed: 137 average time/residue: 0.1628 time to fit residues: 31.8070 Evaluate side-chains 142 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 76 optimal weight: 0.0570 chunk 87 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 460 ASN B 460 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.131398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.107888 restraints weight = 9120.063| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.52 r_work: 0.3022 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7475 Z= 0.207 Angle : 0.651 12.048 10235 Z= 0.313 Chirality : 0.043 0.227 1252 Planarity : 0.005 0.064 1195 Dihedral : 5.016 30.785 1085 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.27 % Allowed : 15.87 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.30), residues: 903 helix: 0.24 (0.22), residues: 660 sheet: None (None), residues: 0 loop : -1.94 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.007 0.001 HIS B 105 PHE 0.014 0.001 PHE A 287 TYR 0.011 0.001 TYR A 514 ARG 0.003 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.897 Fit side-chains REVERT: A 34 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: A 243 CYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8410 (p) REVERT: A 294 ILE cc_start: 0.9075 (mt) cc_final: 0.8842 (mt) REVERT: A 484 LEU cc_start: 0.9078 (tp) cc_final: 0.8701 (tt) REVERT: B 11 ARG cc_start: 0.7418 (mmp80) cc_final: 0.7166 (mmp80) REVERT: B 34 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: B 65 MET cc_start: 0.9279 (mtp) cc_final: 0.9028 (mtp) REVERT: B 267 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: B 294 ILE cc_start: 0.9072 (mt) cc_final: 0.8871 (mt) REVERT: B 484 LEU cc_start: 0.9087 (tp) cc_final: 0.8717 (tt) outliers start: 26 outliers final: 21 residues processed: 133 average time/residue: 0.1613 time to fit residues: 30.8877 Evaluate side-chains 141 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 53 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN B 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.104545 restraints weight = 9313.956| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.59 r_work: 0.3000 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7475 Z= 0.219 Angle : 0.657 11.649 10235 Z= 0.316 Chirality : 0.044 0.224 1252 Planarity : 0.005 0.065 1195 Dihedral : 5.031 30.358 1085 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.27 % Allowed : 17.13 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.30), residues: 903 helix: 0.27 (0.22), residues: 661 sheet: None (None), residues: 0 loop : -1.97 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 572 HIS 0.008 0.001 HIS B 105 PHE 0.014 0.001 PHE B 287 TYR 0.010 0.001 TYR A 81 ARG 0.003 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.798 Fit side-chains REVERT: A 34 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: A 243 CYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8463 (p) REVERT: A 267 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: A 294 ILE cc_start: 0.9078 (mt) cc_final: 0.8852 (mt) REVERT: A 484 LEU cc_start: 0.9094 (tp) cc_final: 0.8716 (tt) REVERT: B 11 ARG cc_start: 0.7430 (mmp80) cc_final: 0.7182 (mmp80) REVERT: B 34 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: B 65 MET cc_start: 0.9294 (mtp) cc_final: 0.9074 (mtp) REVERT: B 484 LEU cc_start: 0.9097 (tp) cc_final: 0.8711 (tt) outliers start: 26 outliers final: 21 residues processed: 133 average time/residue: 0.1754 time to fit residues: 33.2696 Evaluate side-chains 141 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN B 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.131616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.107614 restraints weight = 9211.941| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.55 r_work: 0.3021 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7475 Z= 0.197 Angle : 0.650 11.347 10235 Z= 0.312 Chirality : 0.043 0.225 1252 Planarity : 0.005 0.064 1195 Dihedral : 4.983 30.286 1085 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.02 % Allowed : 17.25 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.30), residues: 903 helix: 0.34 (0.22), residues: 661 sheet: None (None), residues: 0 loop : -1.95 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 572 HIS 0.007 0.001 HIS B 105 PHE 0.014 0.001 PHE B 287 TYR 0.023 0.001 TYR A 514 ARG 0.002 0.000 ARG B 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.762 Fit side-chains REVERT: A 34 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: A 243 CYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8446 (p) REVERT: A 294 ILE cc_start: 0.9074 (mt) cc_final: 0.8849 (mt) REVERT: A 484 LEU cc_start: 0.9076 (tp) cc_final: 0.8697 (tt) REVERT: B 11 ARG cc_start: 0.7424 (mmp80) cc_final: 0.7163 (mmp80) REVERT: B 34 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: B 65 MET cc_start: 0.9299 (mtp) cc_final: 0.9059 (mtp) REVERT: B 484 LEU cc_start: 0.9080 (tp) cc_final: 0.8706 (tt) outliers start: 24 outliers final: 21 residues processed: 131 average time/residue: 0.1581 time to fit residues: 29.6513 Evaluate side-chains 137 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 chunk 64 optimal weight: 0.1980 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN B 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.105888 restraints weight = 9165.391| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.59 r_work: 0.3017 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7475 Z= 0.196 Angle : 0.645 11.071 10235 Z= 0.310 Chirality : 0.043 0.221 1252 Planarity : 0.005 0.063 1195 Dihedral : 4.923 29.895 1085 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.15 % Allowed : 17.63 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.30), residues: 903 helix: 0.41 (0.22), residues: 660 sheet: None (None), residues: 0 loop : -1.97 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 572 HIS 0.007 0.001 HIS B 105 PHE 0.013 0.001 PHE B 287 TYR 0.009 0.001 TYR A 81 ARG 0.001 0.000 ARG A 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3526.95 seconds wall clock time: 63 minutes 24.92 seconds (3804.92 seconds total)